I think it's obvious that Squall is hiding feelings, they hint that all throughout the game.

He gives the cold shoulder when someone asks him something personal, but when it comes to helping innocent people, or shows some type of effection, the team will respond with something like: "wow, I didn't expect to hear that from you" or "Is squall showing some affection?" or whatnot, and of course, he feels violated and retaliates with 'whatever'.

It's not Just towards Rinoa. At different parts he will go out of his way to save his friends. He puts up a defensive shield normally, and you're not really sure what he feels.

Most of the time when Rinoa pisses Squall off, it's because she's trying to 'break his shell'. Squall will not allow this. It would only take something serious for him to break free of it.

That's why, when he 'freaked out' all of the sudden, it was expected. What happens when Rinoa and Squall are united again, he goes back to his old self again. The game was trying to show that Squall actually feared showing his feelings.

I don't believe Squall ever hated her. You can tell when they got into a battle early on in the game and she ran away, all he thought about was what he did wrong.

I strongly believe there were subtle things in the plot hinting towards him liking her. It wasn't an out-of-the-blue thing to me. When I'm playing through this playthrough, I'll jolt down some of those subtleties and post them here.